Differential Expression of ABC Transporter Genes in Brain Vessels vs. Peripheral Tissues and Vessels from Human, Mouse and Rat

Abstract

Background: ATP-binding cassette (ABC) transporters comprise a superfamily of genes encoding membrane proteins with nucleotide-binding domains (NBD). These transporters, including drug efflux across the blood-brain barrier (BBB), carry a variety of substrates through plasma membranes against substrate gradients, fueled by hydrolyzing ATP. The expression patterns/enrichment of ABC transporter genes in brain microvessels compared to peripheral vessels and tissues are largely uncharacterized.

Methods: In this study, the expression patterns of ABC transporter genes in brain microvessels, peripheral tissues (lung, liver and spleen) and lung vessels were investigated using RNA-seq and Wes^TM analyses in three species: human, mouse and rat.

Results: The study demonstrated that ABC drug efflux transporter genes (including ABCB1, ABCG2, ABCC4 and ABCC5) were highly expressed in isolated brain microvessels in all three species studied; the expression of ABCB1, ABCG2, ABCC1, ABCC4 and ABCC5 was generally higher in rodent brain microvessels compared to those of humans. In contrast, ABCC2 and ABCC3 expression was low in brain microvessels, but high in rodent liver and lung vessels. Overall, most ABC transporters (with the exception of drug efflux transporters) were enriched in peripheral tissues compared to brain microvessels in humans, while in rodent species, additional ABC transporters were found to be enriched in brain microvessels.

Conclusions: This study furthers the understanding of species similarities and differences in the expression patterns of ABC transporter genes; this is important for translational studies in drug development. In particular, CNS drug delivery and toxicity may vary among species depending on their unique profiles of ABC transporter expression in brain microvessels and BBB.

Keywords: ABC transporters; RNA-seq; WesTM analysis; across species; brain microvessels; gene expression patterns; peripheral tissues and vessels.

Figure 1

The expression of ABC drug transporter genes in brain microvessels of humans, mice and rats analyzed by transcript per million (TPM) across species.

Figure 2

Heatmap for the levels of ABC transporter gene expression in humans, mice and rats (h for humans; m for mice and r for rats in the graphs): Three samples were used in RNA-seq analyses for cerebral vessels and peripheral tissues and lung vessels from humans, mice and rats. The RNA-seq data were converted to transcript per million (TPM) counts for comparison across species. The means of three samples (TPM counts) were used in the following analysis. (A). Transcript per million counts (TPM) ranking for ABC transporter gene expression in human, mouse and rat brain vessels vs. peripheral tissues and lung vessels. (B). TPM ranking values of hierarchical clustering for ABC transporter gene expression in human, mouse and rat brain vessels vs. peripheral tissues and lung vessels.

Figure 3

Expression of ABC drug transporter genes in cerebral and lung vessels across species. Three samples of cerebral vessels from humans, mice and rats were used in RNA-seq analysis. The RNA-seq data were then converted to transcript per million (TPM) counts for comparison across species. Mean ± SD from three samples was used in the analysis (Table 1, Table 2, Table 3 and Table 4). One-way ANOVA was used for statistical analysis (* p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001).

Figure 4

K-means clustering of RNA-seq data (TPM counts) showing classification of ABC transporter gene expression in brain vessels vs. peripheral tissues. (A). Human brain vessels vs. human lung tissues. (B). Mouse brain vessels vs. mouse peripheral tissues (including mouse liver and spleen tissues). (C). Rat brain vessels vs. rat peripheral tissues (including rat liver and spleen tissues). The 8 clusters in each species correspond to the following: (1) high in brain vessels and low in peripheral tissues, (2) high in brain vessels and medium in peripheral tissues, (3) medium in brain vessels and low in peripheral tissues, (4) high in brain vessels and high in peripheral tissues, (5) medium in brain vessels and medium in peripheral tissues, (6) low in brain vessels and low in peripheral tissues, (7) low in brain vessels and medium in peripheral tissues, (8) low in brain vessels and high in peripheral tissues.

Figure 4

K-means clustering of RNA-seq data (TPM counts) showing classification of ABC transporter gene expression in brain vessels vs. peripheral tissues. (A). Human brain vessels vs. human lung tissues. (B). Mouse brain vessels vs. mouse peripheral tissues (including mouse liver and spleen tissues). (C). Rat brain vessels vs. rat peripheral tissues (including rat liver and spleen tissues). The 8 clusters in each species correspond to the following: (1) high in brain vessels and low in peripheral tissues, (2) high in brain vessels and medium in peripheral tissues, (3) medium in brain vessels and low in peripheral tissues, (4) high in brain vessels and high in peripheral tissues, (5) medium in brain vessels and medium in peripheral tissues, (6) low in brain vessels and low in peripheral tissues, (7) low in brain vessels and medium in peripheral tissues, (8) low in brain vessels and high in peripheral tissues.

Figure 4

K-means clustering of RNA-seq data (TPM counts) showing classification of ABC transporter gene expression in brain vessels vs. peripheral tissues. (A). Human brain vessels vs. human lung tissues. (B). Mouse brain vessels vs. mouse peripheral tissues (including mouse liver and spleen tissues). (C). Rat brain vessels vs. rat peripheral tissues (including rat liver and spleen tissues). The 8 clusters in each species correspond to the following: (1) high in brain vessels and low in peripheral tissues, (2) high in brain vessels and medium in peripheral tissues, (3) medium in brain vessels and low in peripheral tissues, (4) high in brain vessels and high in peripheral tissues, (5) medium in brain vessels and medium in peripheral tissues, (6) low in brain vessels and low in peripheral tissues, (7) low in brain vessels and medium in peripheral tissues, (8) low in brain vessels and high in peripheral tissues.